Gemma C. Atkinson
@gemmaatkinson.bsky.social
Lecturer & group leader in Lund University. Computational microbiologist, mostly working on toxin-antitoxin systems, ribosomes and bacterial defence against phages. Director of the LU-Fold protein structure prediction infrastructure of LU.
Atkinson-lab.com
Atkinson-lab.com
Reposted by Gemma C. Atkinson
Viral AlphaFold Database (VAD) is live in Science Advances
~27,000 predicted viral protein monomers & homodimers
Conserved folds across bacteria, archaea & eukaryotic viruses
New toxin–antitoxin system KreTA uncovered
Vast “functional darkness” remains uncharted
www.science.org/doi/10.1126/...
~27,000 predicted viral protein monomers & homodimers
Conserved folds across bacteria, archaea & eukaryotic viruses
New toxin–antitoxin system KreTA uncovered
Vast “functional darkness” remains uncharted
www.science.org/doi/10.1126/...
The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes
VAD is a Viral AlphaFold Database of protein monomers and homodimers from viruses infecting hosts across the tree of life.
www.science.org
October 2, 2025 at 8:48 AM
Viral AlphaFold Database (VAD) is live in Science Advances
~27,000 predicted viral protein monomers & homodimers
Conserved folds across bacteria, archaea & eukaryotic viruses
New toxin–antitoxin system KreTA uncovered
Vast “functional darkness” remains uncharted
www.science.org/doi/10.1126/...
~27,000 predicted viral protein monomers & homodimers
Conserved folds across bacteria, archaea & eukaryotic viruses
New toxin–antitoxin system KreTA uncovered
Vast “functional darkness” remains uncharted
www.science.org/doi/10.1126/...
Looking forward to this!
Hello everyone! I am pleased to share information on the first ever Computational Structural Virology Symposium, conducted August 4th on zoom and highlighting work in this emerging field. You can register for this event here: forms.gle/CNiqskMwQEuV.... Please re-post!
June 17, 2025 at 2:37 PM
Looking forward to this!
ooo this looks fun, and in ❤️York❤️
Fancy a journey back in time to Roman Eboracum by walking on the city walls?And a visit to the Norman Clifford Tower? A stroll down the Middle Age Shambles? All this whilst enjoying a full immersion into chromosome biology? 🧬 Join us at The Biology & Physics of Prokaryotic Chromosomes!
🦠🧪🧬
🦠🧪🧬
May 19, 2025 at 7:16 AM
ooo this looks fun, and in ❤️York❤️
Really excited to share our resource and analysis of AlphaFold-predicted monomers and homodimers across viruses and phages. Project driven by fab PhD student @rodai.bsky.social and with our great collaborators Joana Pereira @joanampereira.bsky.social and @ninjani.bsky.social
The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes https://www.biorxiv.org/content/10.1101/2025.05.14.653371v1
May 19, 2025 at 6:37 AM
Really excited to share our resource and analysis of AlphaFold-predicted monomers and homodimers across viruses and phages. Project driven by fab PhD student @rodai.bsky.social and with our great collaborators Joana Pereira @joanampereira.bsky.social and @ninjani.bsky.social
Reposted by Gemma C. Atkinson
Two ERC-funded postdoc positions available in the team - one here and second to follow - please repost! jobs.ncl.ac.uk/job/Newcastl...
Research Associate Genetic and functional analysis of Gram positive secretion systems and substrates
Research Associate Genetic and functional analysis of Gram positive secretion systems and substrates
jobs.ncl.ac.uk
April 9, 2025 at 12:29 PM
Two ERC-funded postdoc positions available in the team - one here and second to follow - please repost! jobs.ncl.ac.uk/job/Newcastl...
Reposted by Gemma C. Atkinson
The BASEL collection of E. coli #phages is limited by its host strain. @humollidorentina.bsky.social @damienpiel.bsky.social @aharms485.bsky.social &co use a modified host to add 36 new phages, revealing roles of O-antigen in recognition & R-M systems in immunity @plosbiology.org 🧪 plos.io/4jirGvX
April 8, 2025 at 4:55 PM
The BASEL collection of E. coli #phages is limited by its host strain. @humollidorentina.bsky.social @damienpiel.bsky.social @aharms485.bsky.social &co use a modified host to add 36 new phages, revealing roles of O-antigen in recognition & R-M systems in immunity @plosbiology.org 🧪 plos.io/4jirGvX
Please spread the word! We have an opening in the Atkinson lab for a post-doc with a focus on the molecular mechanisms of microbial immune systems. Can be a fully computational or experimental or hybrid project.
Read more and apply here:
lu.varbi.com/en/what:job/...
#phage #bioinformatics
Read more and apply here:
lu.varbi.com/en/what:job/...
#phage #bioinformatics
Postdoctoral research fellow with a focus on the molecular mechanisms of bacteriophage-host interactions
Description of the Workplace In the Atkinson lab we are interested in making discoveries about protein function and structure, with a focus on bacterial immune system components that protect against b
lu.varbi.com
April 8, 2025 at 6:19 AM
Reposted by Gemma C. Atkinson
Looking forward to attending this conference for the 1st time and co-chairing this session with amazing speakers!
Join us on 2 and 3 April and listen to @gemmaatkinson.bsky.social, @epcrocha.bsky.social , @tatianadimitriu.bsky.social and Tim Blower!
#Microbio25
Join us on 2 and 3 April and listen to @gemmaatkinson.bsky.social, @epcrocha.bsky.social , @tatianadimitriu.bsky.social and Tim Blower!
#Microbio25
Microbes in Combat! Join us at #Microbio25 for Microbial Warfare: Conflicts Between Species, Strains, and Mobile Genetic Elements. Delve into microbial defence mechanisms and the implications for microbial evolution. Registration is still open -
Annual Conference 2025
31 March - 03 April 2025
microb.io
March 29, 2025 at 3:20 PM
Looking forward to attending this conference for the 1st time and co-chairing this session with amazing speakers!
Join us on 2 and 3 April and listen to @gemmaatkinson.bsky.social, @epcrocha.bsky.social , @tatianadimitriu.bsky.social and Tim Blower!
#Microbio25
Join us on 2 and 3 April and listen to @gemmaatkinson.bsky.social, @epcrocha.bsky.social , @tatianadimitriu.bsky.social and Tim Blower!
#Microbio25
Reminder about two open positions:
1) tenure track group leader position on data driven infection research lu.varbi.com/en/what:job/...
2) post-doc in mine/Vasili's join team lu.varbi.com/en/what:job/...
#phagesky #microsky
1) tenure track group leader position on data driven infection research lu.varbi.com/en/what:job/...
2) post-doc in mine/Vasili's join team lu.varbi.com/en/what:job/...
#phagesky #microsky
Postdoctoral research fellow with a focus on the molecular mechanisms of bacteriophage-host interactions
Description of the Workplace In the Atkinson lab we are interested in making discoveries about protein function and structure, with a focus on bacterial immune system components that protect against b
lu.varbi.com
March 25, 2025 at 7:05 AM
Reminder about two open positions:
1) tenure track group leader position on data driven infection research lu.varbi.com/en/what:job/...
2) post-doc in mine/Vasili's join team lu.varbi.com/en/what:job/...
#phagesky #microsky
1) tenure track group leader position on data driven infection research lu.varbi.com/en/what:job/...
2) post-doc in mine/Vasili's join team lu.varbi.com/en/what:job/...
#phagesky #microsky
Please spread the word! We have an opening in the Atkinson lab for a post-doc with a focus on the molecular mechanisms of microbial immune systems. Can be a fully computational or experimental or hybrid project.
Read more and apply here:
lu.varbi.com/en/what:job/...
#phage #bioinformatics
Read more and apply here:
lu.varbi.com/en/what:job/...
#phage #bioinformatics
Postdoctoral research fellow with a focus on the molecular mechanisms of bacteriophage-host interactions
Description of the Workplace In the Atkinson lab we are interested in making discoveries about protein function and structure, with a focus on bacterial immune system components that protect against b
lu.varbi.com
March 19, 2025 at 8:51 PM
Please spread the word! We have an opening in the Atkinson lab for a post-doc with a focus on the molecular mechanisms of microbial immune systems. Can be a fully computational or experimental or hybrid project.
Read more and apply here:
lu.varbi.com/en/what:job/...
#phage #bioinformatics
Read more and apply here:
lu.varbi.com/en/what:job/...
#phage #bioinformatics
Bioinformatics junior group leader position in Lund, specialising in infection and/or epidemiology. These are really nice positions with generous support. Please spread the word to anyone who might be interested in becoming our colleague! lu.varbi.com/en/what:job/...
Associate Senior Lecturer (DDLS fellow) in data driven epidemiology and biology of infection
Lund is strategically positioned close to the continent, hosting major national and European research infrastructures, such as MAX.IV Laboratory and the European Spallation Source (ESS). In the field
lu.varbi.com
March 7, 2025 at 4:52 PM
Bioinformatics junior group leader position in Lund, specialising in infection and/or epidemiology. These are really nice positions with generous support. Please spread the word to anyone who might be interested in becoming our colleague! lu.varbi.com/en/what:job/...
Post-doc opportunities! Wet/dry/hybrid projects available in my group. Drop me an email with CV if interested.
www.scilifelab.se/research/pul...
www.scilifelab.se/research/pul...
Pulse - Application
Application PULSE postdoc applicants have the opportunity to choose between an academic or an entrepreneurial track. Both fellowship tracks will include advanced training in research and transferable ...
www.scilifelab.se
February 26, 2025 at 8:06 AM
Post-doc opportunities! Wet/dry/hybrid projects available in my group. Drop me an email with CV if interested.
www.scilifelab.se/research/pul...
www.scilifelab.se/research/pul...
Excited to share that our paper on locus visualisation tool LoVis4u is out! Entirely driven by fantastic PhD student Artyom Egorov @egorov.bsky.social academic.oup.com/nargab/artic...
LoVis4u: a locus visualization tool for comparative genomics and coverage profiles
Abstract. Comparative genomic analysis often involves visualization of alignments of genomic loci. While several software tools are available for this task
academic.oup.com
February 25, 2025 at 7:27 AM
Excited to share that our paper on locus visualisation tool LoVis4u is out! Entirely driven by fantastic PhD student Artyom Egorov @egorov.bsky.social academic.oup.com/nargab/artic...
Some exciting news about our structure prediction infrastructure LU-Fold: we have joined forces with SciLifeLab to improve accessibility to technologies and expertise. Read more here nbis.se/news/LUfold
NBIS - LU-Fold and NBIS join forces to Enhance Protein Structure Prediction Services at SciLifeLab
nbis.se
January 23, 2025 at 11:10 AM
Some exciting news about our structure prediction infrastructure LU-Fold: we have joined forces with SciLifeLab to improve accessibility to technologies and expertise. Read more here nbis.se/news/LUfold
Big day for the family. Today one of these two became a full professor. Nice job @hauryliuk.bsky.social !
January 16, 2025 at 6:46 PM
Big day for the family. Today one of these two became a full professor. Nice job @hauryliuk.bsky.social !
Such a good VH-GCA lab symposium day to round off the year!
December 19, 2024 at 3:23 PM
Such a good VH-GCA lab symposium day to round off the year!
Grateful to the Swedish Research Council (Vetenskapsrådet) for funding a 3 year project on antibiotic resistance & phages in my group. If you're looking for a post-doc position in 2025, have a phagey background, & are interested in combining wet and dry research then keep a look out for an ad soon!
December 3, 2024 at 2:30 PM
Grateful to the Swedish Research Council (Vetenskapsrådet) for funding a 3 year project on antibiotic resistance & phages in my group. If you're looking for a post-doc position in 2025, have a phagey background, & are interested in combining wet and dry research then keep a look out for an ad soon!
Any tips?
Gemma, we are interested in visualizing the alignment between two plasmids in a circular format. Could you recommend us a tool?
December 1, 2024 at 4:54 PM
Any tips?
Reposted by Gemma C. Atkinson
Exciting times! Our latest preprint is now live 🤩!
After nearly 16 yrs of running my lab, I truly believe this is one of the most significant contributions we've made. It offers fresh hypotheses about how pandemic Vibrio cholerae spreads globally. Let’s dive in!🧵..1/n
www.biorxiv.org/content/10.1...
After nearly 16 yrs of running my lab, I truly believe this is one of the most significant contributions we've made. It offers fresh hypotheses about how pandemic Vibrio cholerae spreads globally. Let’s dive in!🧵..1/n
www.biorxiv.org/content/10.1...
Diverse phage defence systems define West African South American pandemic Vibrio cholerae
Our understanding of the factors underlying the evolutionary success of different lineages of pandemic Vibrio cholerae remains incomplete. Interestingly, two unique genetic signatures define the West ...
www.biorxiv.org
November 25, 2024 at 2:27 PM
Exciting times! Our latest preprint is now live 🤩!
After nearly 16 yrs of running my lab, I truly believe this is one of the most significant contributions we've made. It offers fresh hypotheses about how pandemic Vibrio cholerae spreads globally. Let’s dive in!🧵..1/n
www.biorxiv.org/content/10.1...
After nearly 16 yrs of running my lab, I truly believe this is one of the most significant contributions we've made. It offers fresh hypotheses about how pandemic Vibrio cholerae spreads globally. Let’s dive in!🧵..1/n
www.biorxiv.org/content/10.1...
So fab to hear when people find our lab tools useful. Now that he’s on Bluesky, I can tag Artyom @egorov.bsky.social , the amazing PhD student who made iLund4u and loVis4u
Really missed the sense of daily discovery of new papers and tools you used to get on the other place. Moved over a few days ago and already finding so much, and exactly what I've been looking for!
Sharing new tools made by Artyom Egorov in my group!
1) loVis4u sensitively compares & visualises #phage or #plasmid seqs with beautiful vector graphics www.biorxiv.org/content/10.1...
2) iLund4u finds diversity hotspots/islands encoding eg virulence/ defence systems www.biorxiv.org/content/10.1...
1) loVis4u sensitively compares & visualises #phage or #plasmid seqs with beautiful vector graphics www.biorxiv.org/content/10.1...
2) iLund4u finds diversity hotspots/islands encoding eg virulence/ defence systems www.biorxiv.org/content/10.1...
November 23, 2024 at 7:25 PM
So fab to hear when people find our lab tools useful. Now that he’s on Bluesky, I can tag Artyom @egorov.bsky.social , the amazing PhD student who made iLund4u and loVis4u
Reposted by Gemma C. Atkinson
Anyone looking for an assistant professor position in biodiversity research? Not one but three positions available at Stockholm U:
www.su.se/department-o...
www.su.se/department-o...
Faculty of Science is recruiting Assistant Professors in Biodiversity - Department of Ecology, Environment and Plant Sciences
Faculty of Science is recruiting Assistant Professors in Biodiversity - Department of Ecology, Environment and Plant Sciences
www.su.se
November 22, 2024 at 2:46 PM
Anyone looking for an assistant professor position in biodiversity research? Not one but three positions available at Stockholm U:
www.su.se/department-o...
www.su.se/department-o...
Sharing new tools made by Artyom Egorov in my group!
1) loVis4u sensitively compares & visualises #phage or #plasmid seqs with beautiful vector graphics www.biorxiv.org/content/10.1...
2) iLund4u finds diversity hotspots/islands encoding eg virulence/ defence systems www.biorxiv.org/content/10.1...
1) loVis4u sensitively compares & visualises #phage or #plasmid seqs with beautiful vector graphics www.biorxiv.org/content/10.1...
2) iLund4u finds diversity hotspots/islands encoding eg virulence/ defence systems www.biorxiv.org/content/10.1...
October 24, 2024 at 11:12 AM
Sharing new tools made by Artyom Egorov in my group!
1) loVis4u sensitively compares & visualises #phage or #plasmid seqs with beautiful vector graphics www.biorxiv.org/content/10.1...
2) iLund4u finds diversity hotspots/islands encoding eg virulence/ defence systems www.biorxiv.org/content/10.1...
1) loVis4u sensitively compares & visualises #phage or #plasmid seqs with beautiful vector graphics www.biorxiv.org/content/10.1...
2) iLund4u finds diversity hotspots/islands encoding eg virulence/ defence systems www.biorxiv.org/content/10.1...
Very proud of my life and science other half Vasili Hauryliuk @hauryliuk.bsky.social being awarded the Göran Gustafsson prize in molecular biology from the Royal Swedish Academy of Sciences! www.kva.se/nyheter/33-m...
March 1, 2024 at 7:03 AM
Very proud of my life and science other half Vasili Hauryliuk @hauryliuk.bsky.social being awarded the Göran Gustafsson prize in molecular biology from the Royal Swedish Academy of Sciences! www.kva.se/nyheter/33-m...
Senior lectureship available in Lund with specialisation in cryo-EM. Come and join us and have fun playing around with the brand new Glacios 2 #cryoem lu.varbi.com/en/what:job/...
February 23, 2024 at 3:46 PM
Senior lectureship available in Lund with specialisation in cryo-EM. Come and join us and have fun playing around with the brand new Glacios 2 #cryoem lu.varbi.com/en/what:job/...
Now we have a bioinformatics PhD position In my group in Lund to work on the same fun #phage defence project! Read more and apply here: lu.varbi.com/en/what:job/... deadline March 5th
Three-year postdoc available on anti-phage defense systems and phage biocontrol of phytopathogenic Ralstonia solanacearum at Helsinki (FIN) in collaboration with @hauryliuk.bsky.social and gemmaatkinson.bsky.social. Application deadline 29.2.2024. #phagesky #microsky jobs.helsinki.fi/job/Helsinki...
February 5, 2024 at 4:02 PM
Now we have a bioinformatics PhD position In my group in Lund to work on the same fun #phage defence project! Read more and apply here: lu.varbi.com/en/what:job/... deadline March 5th